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- PDB-3gvu: The crystal structure of human ABL2 in complex with GLEEVEC -

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Basic information

Entry
Database: PDB / ID: 3gvu
TitleThe crystal structure of human ABL2 in complex with GLEEVEC
ComponentsTyrosine-protein kinase ABL2
KeywordsTRANSFERASE / Tyrosine kinase / ABL / Abelson murine leukemia viral oncogene / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / positive regulation of establishment of T cell polarity / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / positive regulation of establishment of T cell polarity / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / cellular response to retinoic acid / RAC1 GTPase cycle / phosphotyrosine residue binding / Negative regulation of FLT3 / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / epidermal growth factor receptor signaling pathway / protein modification process / regulation of autophagy / positive regulation of neuron projection development / actin filament binding / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / protein tyrosine kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / protein kinase activity / cell adhesion / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-STI / Tyrosine-protein kinase ABL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsUgochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Filippakopoulos, P. / Roos, A. / Pike, A.C.W. ...Ugochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Filippakopoulos, P. / Roos, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human ABL2 in complex with GLEEVEC
Authors: Salah, E. / Ugochukwu, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Knapp, S.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5313
Polymers33,5431
Non-polymers9872
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tyrosine-protein kinase ABL2
hetero molecules

A: Tyrosine-protein kinase ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0616
Polymers67,0872
Non-polymers1,9744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6150 Å2
ΔGint-28 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.460, 99.440, 87.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

21A-250-

HOH

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Components

#1: Protein Tyrosine-protein kinase ABL2 / Abelson murine leukemia viral oncogene homolog 2 / Abelson-related gene protein / Tyrosine kinase ARG


Mass: 33543.359 Da / Num. of mol.: 1 / Fragment: Protein kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL2 / Plasmid: pFB-LIC-Bse / Cell line (production host): High5 Insect cell / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P42684, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O / Comment: medication, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.88 Å
DetectorType: MAR225 / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.05→43.9 Å / Num. obs: 24490 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 12.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.2 / Num. unique all: 12308 / Rsym value: 0.445 / % possible all: 95.5

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FPU.pdb

1fpu


Resolution: 2.05→43.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.08 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22644 1244 5.1 %RANDOM
Rwork0.18942 ---
all0.19135 23225 --
obs0.19135 23225 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.411 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å20 Å2
2---1.5 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 74 149 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222355
X-RAY DIFFRACTIONr_bond_other_d0.0020.021571
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9893205
X-RAY DIFFRACTIONr_angle_other_deg1.0343.0053770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15824.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70815380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.788158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212598
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02471
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.53551377
X-RAY DIFFRACTIONr_mcbond_other1.8365554
X-RAY DIFFRACTIONr_mcangle_it5.86972220
X-RAY DIFFRACTIONr_scbond_it7.7899978
X-RAY DIFFRACTIONr_scangle_it8.23811981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 71 -
Rwork0.281 1602 -
obs--93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.93760.0999-0.89652.07341.05745.3233-0.04020.2513-0.0040.02460.01360.0428-0.00630.02580.02660.01-0.01020.01730.028-0.01130.033813.63084.175911.5276
22.42241.50660.37095.58063.02414.32770.0462-0.01230.12780.48460.0238-0.06630.20210.1331-0.070.085-0.0105-0.02450.02510.00090.015719.976417.556434.8369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A269 - 367
2X-RAY DIFFRACTION2A368 - 546

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